TY  - JOUR
A1  - Dell'Ampio, Emiliano
A1  - Meusemann, Karen
A1  - Szucsich, Nikolaus Urban
A1  - Peters, Ralph S.
A1  - Meyer, Benjamin
A1  - Borner, Janus
A1  - Petersen, Malte
A1  - Aberer, Andre J.
A1  - Stamatakis, Alexandros
A1  - Walz, Manfred G.
A1  - Minh, Bui Quang
A1  - Haeseler, Arndt von
A1  - Ebersberger, Ingo
A1  - Pass, Günther
A1  - Misof, Bernhard
T1  - Decisive datasets in phylogenomics : lessons from studies on the phylogenetic relationships of primarily wingless insects
T2  - Molecular biology and evolution
N2  - Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. In order to get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies using an extended transcriptome dataset.Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive datasets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we employed Four-cluster Likelihood-Mapping (FcLM) to measure the degree of congruence among genes of a dataset, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated with neither functional class assignment of these genes, nor with model misspecification due to unpartitioned analyses. The herein analyzed dataset is the currently largest dataset covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. While this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artefacts.
KW  - phylogenomics
KW  - ESTs
KW  - likelihood quartet mapping
KW  - conflicting hypotheses
KW  - Entognatha
KW  - Nonoculata
KW  - Ellipura
KW  - Protura
KW  - Diplura
KW  - Collembola
KW  - missing data
Y1  - 2013
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/40347
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-403478
UR  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879454
UR  - http://mbe.oxfordjournals.org/content/early/2013/10/18/molbev.mst196
SN  - 0737-4038
SN  - 1537-1719
N1  - © The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
VL  - 31
IS  - 1
SP  - 239
EP  - 249
PB  - Oxford Univ. Press
CY  - Oxford
ER  -